Slashdot Mirror
Distributed Computing Attacking SARS
fwc writes "D2OL has added a SARS Target to it's distributed computing project which locates potential drug candidates for several viruses. At this point, I've replaced SETI@Home at least temporarily on all of my Boxen. There are clients available for Linux, Solaris, Mac OS X, and of course Windows."
Looks more usefull then finding the odd alien out there :P
-- signed for your pleasure --
If everyone stops doing SETI@home and moves to battling the SARS problem then we may miss a vital signal from outer space from an alien race that has a cure to SARS and all the other nasties roaming this planet!
... I guess
I wonder when my United Devices client (ud.com) is gonna add that project... It's currently working on smallpox and cancer...
;)
Should I change projects? Switch UD in favor of D2OL or what? And why?
Any technology distinguishable from magic, is insufficiently advanced.
Who owns the results once they've been calculated? Who gets paid royalties when a drug is developed from this data? I'm not going to donate my CPU time if SARS sufferers have to pay royalties (either directly or indirectly) to GlaxoSmithcline or the US Government (which IMHO isn't any better than a multinational corporation) for their medication.
Unless the results are released into the public domain or at least licensed under a BSD- or GPL-style license, I'm not touching it.
OLPC Australia
Unfortunately, finding a target binding site for a potential drug is years away from actually having a useful cure...
I know how to cure SARS.
You give 8 of the most powerful businessmen in America SARS.
In two months, there will be 3 or 4 different cures.
/^[A-Z0-9._%+-]+@[A-Z0-9.-]+\.[A-Z]{2,4}$/i
How do all of you out there feel about contributing your computing cycles to the private sector? Previous iterations of this idea have been through nonprofit/university research institutions, but this new post seems to be private enterprise driven. As noble the goal D2OL is working towards is, i still feel odd about the whole idea. I pose the following question to the general Slashdot community: How do you feel about your computing cycles being used for the research and development of pharmaceuticals (or any other imaginable private sector application) and said company reaping tremendous profits from this show of goodwill?
If they find the correct drug against SARS, will it be free? or will it be patented and only the rich countries will use it??
Here's a question.. Suppose i download this thingummy and run it and jackpot, a miracle cure for SARS unrolls in front of my eyes. Do I have any sort of intellectual property rights over my discovery? And do I have the right to prevent the distributed software Im running from connecting back to the server and giving them the good news?
Does this mean I might win the Nobel Prize???
Not that I'm going to do anything like that. Just wondering if the guys behind the thing have thought through the legal issues.
I have found a truly wonderful proof of Fermat's Last Theorem, but unfortunately this sig is too small to contain it.
I'm not sure that this project (as it is now) will be all that useful. Alot of it appears to be hinging on generous speculation.
I'm not a virologist, but as far as I remember, drug-directed approaches haven't been notably successful with attacking coronaviruses (ever hear that "medicine can't cure the common cold", anyone?) -- and to confuse things more, this one seems to be very atypical.
Also, from what I know about the anti-virals that have shown some efficacy against these type of SS-RNA viruses, they've been directed at nucleic acids, not at product-proteins. Ribavirin, which was initially hoped to be the "magic bullet" to stop SARS is a nucleoside analogue (purine? I don't remember). I haven't heard of an effective intervention that disrupts the protein envelope or synthesis.
Additionally, this group is assuming that the causitive agent of SARS has correctly been isolated and identified in the first place, which isn't certain by any means.
Aiming computing power towards a worthy goal like this can't hurt, but I question how effective it really will be. I guess the computer-types can just tweak the parameters as the biomed-folks find out more on their end.
Download the SARS genetic sequence here.
I've heard you can run it under wine but can't be bothered messing with it.
This slashdotting of such a site shows the need of a new distributed computing project. I wish to propose that we all sit down and share our cpu cycles to prevent slashdotting. How about we call the project "SARS: Some people Are likely to Risk Slashdotting this project" (Ok, I know that was a lame attempt at a name, but try coming up with a better one instead of complaining :P )
It would in essence work the way that we'd all put aside ~200k disk space and ~5k bandwidth for storing the most recently posted websites and files on our computers, then people could put together impromptu mirrors from this distributed project and behold! No more slashdottings of sites, articles and programs that one actually wants to read or download!
So, who's with me on this trek into the land where no slashdotter has ever ventured before?
Anyone?
If you're already searcing for E.T. and not a cure for cancer, why would you search for a cure for SARS? SARS is scary because it's new not because it's a currently uncontrollable viral disease, we've got loads of them. HIV/AIDS, TB, the common cold. Somwhere between 80% and 95% recover quite nicely from SARS, IIRC 500,000 die each year of the flue, you don't see us jumping around over that.
Disclaimier: I'm not saying SARS shouldn't be fought, all disease should, but let's all get some perspective.
(To back some of this up with a _little_ more reliable resource found through Google, look here)
Look a monkey!
media hype?
Looks more usefull then finding the odd alien out there :P
/.ers called CIC.
Now if they could come up with a Distributed Computing Project to help with a socially dibilitating disease affecting millions of geeks and
Chronic Invoulntary Celebacy.
There are much more dangerous illnesses than SARS which affect much more people. There are 2000 people sick with SARS but 40 million with AIDS. And the death rates for AIDS is 100 % percent. The numbers for cancer are even higher (not the death rates).
This seems to be rather a angst-hyped PR champain instead of real science. The problems we have now are elsewhere.
Owner of a Mensa membership card.
I'd be inclined to think about this one. Just a related matter. If you look at the spread of HIV around the world, the rate is slower and the powers that be may be less inclined to 1) fund research for cures or vaccines, and 2) probably more importantly less inclined to distribute treatment around the world because it has less chance of affecting them. In short, it may be something like: lets cure the world before this highly infectious disease becomes a problem for us. HIV is much more manageable, we'll let those countries take care of it themselves. If a cure for SARS is found, needless to say several things will happen: -the drugs will be made cheaply available -they will be distributed more quickly than ever before -ALL countries and all classes/races/religions will get them -the drug companies may not be able to swing a patent and expensive license manufacturig rights. How about doing this for AIDS in Africa and other areas where HIV is rife. There is no doubt it will affect everybody. It is just a little further down the road. As tragic as it is, SARS is something that will I hope break the barriers between nations (just like a funeral is the best way to get a family together). There is nothing for individual nations to play for with a visibly threatening global problem like SARS. It is just a damn shame that HIV and the environment get a back seat because those in authority refuse to see further than the tips of their noses (or election campaigns.)
You know how easy it is to catch a cold right? Well, SARS is like that, a cold. It's easy to catch. There's a damn good reason for all this hype. No one talked about SARS in china for months until it went totally out of control and people didn't realize that they should be taking basic precautions.
SARS would have absolutely no problem killing the same numbers of people if it managed to get 'free' of the quarantines and stuff
Also, Michael Mooor is a dumbass, and he has his math backwards. The more scared we are, the less we consume. SARS is death to tourism and the like in Asia, and it makes people stay home to avoid it.
9/11 certanly didn't boost the economy.
autopr0n is like, down and stuff.
I saw a report yesterday, either BBC or CNN, that WHO now believes the fatality rate of SARS will be about 10-15%. Much higher than previously believed (this was after China went public with their info)
Je ne parle pas francais.
When it comes to diseases, early overreaction is good. At an early stage there is little information about exactly how dangerous this particular disease might turn out to be. At the same time, containing the disease at this stage is easy. All you might need to do is quarantine half a dozen people.
Of course, as the disease progresses and the actual severity of the epidemic is assessed, we can update our procedures to make it less or more stringent as the need might be.
This is the same reason why firemen overreact to fire alarms by the way. It is so much easier to contain a fire in the first three-five minutes that is worth driving recklessly to the scene of the fire, even though 95% of the time they turn out to be false alarms.
that all these distributed projects are actually doing what they're supposed to?
Would you notice it if my long-lasting-no-results-yet-but-soon-for-sure distributed project for an AIDS vaccine were actually a rendering farm for animated kiddie porn movies?
How small a thought it takes to fill a whole life
The way the world is reacting to SARS is much like the way it would have reacted to the 1918-1919 flu, if we'd had the public health infrastructure then that we do now. And that reaction would have saved millions of lives
The correlation between ignorance of statistics and using "correlation is not causation" as an argument is close to 1.
Ever did the math ?
In an average year, 10 to 20 percent of the people get infected with some form of influenza. There are different strains, so for arguments sake lets say 0.5% of the people gets infected with the SARS virus (very conservative estimate).
Based on the current deaths, approximately 3-4% of the people who get infected, actually dies. (experts are actually arguing that this number may be higher).
On a population of 6 billion, that is approximately 900,000 people.(or to put it in a US perspective 75,000 people)
Normal influenza kills mostly the weak and old. SARS does not. So far it has killed a lot of nurses and doctors.
Something to think about before making a decision on whether or not to participate.
You can argue patents all you want but in order for the pharmaceutical industry to function the intellectual property right of drug research companies most be sacrosanct. Billions of dollars are spent every year on pharmaceutical research and if the is no return on investment then there won't be billions of dollars to spend next year. I realize that there are government grants but that is not were most of the money to fund research comes from most if it comes from the money made from the previous successful drug. I know it sounds cruel to say you can't make this drug because you can't afford the patent rights but its better then having there be no drug research at all.
Just so you all know, this is about as fruitful as SETI, so don't go giving up on that just because this "sounds" like it'll be more important or yield a more relevant result. It won't. I work on this type of protein modelling and drug-protein interaction research. The state of the art is that anything produced by your client is going to be at best a wild guess at what the protein looks like or what interactions the drug will make with the protein.
The "scoring" that your results are based on is just how nice the energy is of the final folded protein. This is flawed in a couple of ways, first it means that we need to know nearly everything about protein folding energetics and calculate it with a tidy formula (not yet...but we're getting there) and it means that the folds chosen by the algorithm to test for these energies are all the possible folds (last best guess is that we only know about 80% of all folds)...and then if you're going to try to use this for docking a drug molecule...you open a whole new can of drug-protein interaction knowledge necessary.
SETI actually has a better scoring method for finding a "hit" and while the result (hey, look radio from space) isn't as tangible as killing a virus...I'd say stick with the SETI or try and break the XBox number....or find some more prime numbers. At this point, distributed protein folding/docking isn't just fishing in the dark, it's fishing in the dark in Death Valley.
Mordor...a magical, mythical land where women are more rare than dragons--but where every man would rather find a dragon
...last I heard, the development of a new drug costs billions of dollars. Now, it's all fine and dandy to get on your moral high horse and say that "no cure is better than an expensive cure", but at the end of the day, the money to create the drugs has to come from somewhere. So if you really believe what you're saying, I see one option - see if a VC or banker will float you a loan based on the premise that "I won't be paying you back the $1,378,422,596.83 it took to research and design the drug because it just isn't important, don't you see that poor people need these drugs more than you need your money back?" If you do find somebody who'll do that, let me know, I could use some free money too..
Not that pharmcos won't do some pretty low things, but really, with the expenses we're talking about, basic economics can explain a whole lot of it.
Facts do not cease to exist because they are ignored. - Aldous Huxley
UNAIDS sez if we (the world) spend $10 billion a year for 20 years, it will steadily decrease the number of infections. Right now, we're spending more like $1.2 billion a year, and AIDS is going crazy all over the world. Are we not spending that money because of a focus on SARS? No. We're not spending it because the countries who would be paying $5-6 billion of that are not the ones with 40% infection rates, so they simply don't care. SARS doesn't really affect that.
On the other hand, if you read a history of the AIDS outbreak in the US, you'll find that people wish there had been a much stronger response right from the start. If we had reacted to AIDS the way we reacted to SARS, that $10 billion/year wouldn't be necessary right now -- and most of those 40 million people wouldn't have the disease.
World Health Organization issued a travel advisory
(another article
on Yahoo.)
To be honest with you, I have not taken the TTC (subways or buses) for a long time now so I do not know if there are many people wearing masks there, but on the streets I have only seen two people in the last month actually wearing surgical masks. On the radio (CFRB 1010) there was a discussion of a baseball game from where shots were broadcasted widely displaying a person wearing a mask, with headlines like "In Toronto, Fear Strikes Out ". The host from the radio was on that game and he only saw one (1) person wearing a mask out of thousands of people there. The camera-man concentrated his attention on that person.
Have you seen the shots from Baghdad, where supposedly thousands of Iraqi people were cheering while the US Marines took down Saddams statue? Later in the news they actually showed wide shots of that scene, and it became clear there were only a handfull of people in the area.
This is the same tactics used by the news crews for the single purpose of maintaining attention of millions of people on something that is not that newsworthy but something that can be blown out of the proportions and something that will boost news channels' ratings.
I live in Toronto and I swear to you there is no uncontrolably spread disease here, the offices are not closing, the restaurants and hotels are not closing business is as usual, people are not staying home out of fear but there are a few thousand people on quarantine, most of which will never show any symptoms.
Since last week there was no new cases of SARS in Toronto and the only deaths that occured (19 I think) can be attributed to SARS striking on the older people with some other health problems.
The only thing that WHO achieved was creating massive desinformation and boosting cnn and bbc audiences for the past month and costing Toronto travel industry hundreds of millions of dollars in damage. Really, last year, about 2000 people died in Toronto from flue, but we did not hear about this on cnn.
There are over 5000000 people in Toronto area and there are about 200 people that have SARS, that is 1/50000 of 1 percent. 19 of the sick people died. So far this means about 10% mortality rate for a disease that is statistically so rare, that anyone will have better chances of been killed by a lightning bolt than getting it. Hell, there are more chances of been violently murdered somewhere in Texas than getting SARS in Toronto. Maybe WHO should post a travel advisory about that.
You can't handle the truth.
What benighted fool came up with "Severe Acute Respiratory Syndrome"? Severe and acute mean the same thing.
Not in that context. In the medical community, when a disease is categorized as 'acute' it means the disease has a rapid onset and becomes a problem quickly, as opposed to a 'chronic' disease, which implies a long duration.
Mod down people who tell people how to mod in their sigs
Ebola usually requires some kind of bodily fluid/tissues swap with an infected person.
There's also a reason why "hemorrhagic fever" bugs like Ebola tend to burn themselves out... they are extraordinarily lethal, and quickly kill their host; Ebola has a 90% mortality (compared to 6-12% for SARS). When a virus is too hard on its host, it lessens the opportunity to spread itself.
AIDS is a good example of a successful high-mortality bug... but you can stay alive and asymptomatic for so very long, that spread is virtually assured if you are uncautious.
SARS looks so much like the common cold, that even experienced clinicians have difficulty differentiating it from other bugs. That is, of course, until it's too late. SARS could be a real problem... significant mortality rate, easy to spread, poorly understood, and, like West Nile, NO treatment (well, some advocate treating West Nile with interferons... but the side effects of those drugs are terribly unpleasant; the treatment is almost worse than the disease).
It's nice that they're taking this thing seriously; any money spent on containment is probably well-spent indeed. If they can determine that this bug has no animal reservoir, it could even be eradicated. Till then, public panic serves no one, but public caution is NOT a bad thing.
Even if a man chops off your hand with a sword, you still have two nice, sharp bones to stick in his eyes.
/.ers should be at the forefront in the fight againts SARS for their best interest. It's a known fact that a lot of /.ers are afflicted with SARS (Severe Absence of Romance and Sex).
:)
Oh, you're talking of another kind of SARS.OK, nothing anymore important here. Move on.
"I'll have a witty
SARS has a mortality rate of more than 10% so far in Singapore.
In the past century, there has not been any other infectious disease that has spread so fast and consumed medical and political resources of affected countries so fast.
Just because your country has not been significantly affected (so far) does not mean that this is a minor problem.
It's still early in the progression of SARS. If there are no good public health measures to limit the spread of SARS, it's entirely conceivable that the entire world would be infected by 2005. Even assuming that the mortality sticks at 10% or so, that's a heck of a lot of dead people.
Sometimes this goes as high as 20% in places like Hong Kong, in Canada its around 15%, the 5% are fake government figures.
SARS mortality rate/Death Rate
why dont you read what some actual doctors are saying. Also take into account that SARS is mutating constantly, which means its becoming more deadly everyday, the death rate is rising due to this mutation, as the virus gets smarter it learns how to more efficiently destroy our immune system.
Do your research begore you come up with some numbers.
If you use Linux, please help development of Autopac
I work in Emergency Services, and have already had to deal with TWO suspected cases of SARS. Speaking as a physician, I'll donate my computing cycles, absolutely. The sooner a treatment is brought out, the better.
Here's how I feel about it: I hate having someone come into my ER when I have nothing to offer them. I feel a powerful ethical and professional obligation to take care of people, and do whatever I can for them. I do my best for each and every single patient I see, even if it's somebody who has been through maximal surgery/chemo for their cancer, and has literally reached the end of what medical science can do for them. For such folks, sometimes all I can do is hold their hand and offer a little reassurance, but at least it's SOMETHING. I hate having someone die right in front of me, and being powerless to prevent it. Call it a God complex if you want... I call it wanting to be able to help people. Having people die, and having nothing to say and no way to say it... well, that bothers me, call me crazy.
I don't particularly mind not having a cure for the common cold... a cold is an annoyance, nothing more. I very much DISLIKE not having a treatment for a lethal condition.
I personally don't care who develops the cure... Pharmcos are often painted as evil opportunists that prey on the illnesses of others... I disagree. I like Pharmcos, because they keep my arsenal full, which makes me MUCH more effective at my job. I don't accept Hawaii trips from them, but I'll accept lunch and a couple of pens if they're going to give me some clinically useful information (and hell, I have to write with something). I resent the AMA (I am NOT a member, BTW, for this reason and others) preaching to me about the "unethical behavior" of having dealings with drug reps. Do they really think I'm going to sell out my ethics, my oaths, and my patients because somebody took me to dinner?? I'm sorry, but that's a fucking insult.
I prescribe what I want, within the standard of care, regardless of what drug reps say. I always use cheap if I can, expensive if cheap won't work... but I like the fact that Pharmcos give me tools to take better care of patients.
The sooner a cure for SARS shows up, the happier I'll be.
Even if a man chops off your hand with a sword, you still have two nice, sharp bones to stick in his eyes.
The point about SARS is not how many people it has killed relative to something like your example of murders in Texas. Murders in Texas are not particularly contagious.
The purpose of WHO's advisories is to limit the spread of a contagious disease. It's not really targeted at individuals to tell them that they may be in danger if they go to Toronto - the point is to stop the spread of the disease. However, the disease is ultimately spread by individuals, and to stop it spreading, you ultimately need to prevent individuals from acting as vectors for the disease. That means issuing advisories telling them not to travel to certain regions, and it means quarantining people who may be infected, even though you know that most of them are not.
Unfortunately, individuals aren't very good at recognizing and respecting risks to a global population, and they tend to want to personalize it - which leads to the faulty logic that since the SARS risk to an individual travelling to Toronto is low, it is therefore OK to travel to Toronto.
This is a little like saying that since my personal taxes are small relative to my country's total tax revenues, that I don't need to pay them. The point is that disease containment, like taxes, only works if everyone complies.
BTW, the truth about Toronto specifically, as I understand it, is that its quarantine practices originally weren't up to scratch, and it allowed e.g. exposed health care workers to wander freely amongst the population - attending church, for example. It's at least partially these lapses in containment procedure that have led Toronto to have one of the largest SARS-infected populations on the planet, which is why it was slapped with a WHO warning. The warning is the result of Toronto's health care system and government not originally taking the problem seriously enough.
It's hard to say for sure, but SARS simply doesn't seem that deadly. With worse hygiene and containment certainly far more people would be infected, but it's unlikely such a huge percentage of them would die. Currently fatality rates are in the 2-4% range. Even if that'd double to 4-8% without modern medical care, that's still not near 40%
The Spanish Flu of 1918-1919 had a mortality rate of about 4% which is similar to what we're seeing with SARS. It infected a fifth of the world's population. The U.S. was one of the countries least devastated by the pandemic. But even here 20,000,000 Americans came down with the flu, with 850,000 deaths resulting. Which means that flu killed more Americans than died in all the wars of the twentieth century.
Like SARS, this one originated in China as well. It started as a virus passed from birds to pigs. (They know because in 1997 someone exhumed the body of a soldier who died of it in 1918 and sequenced some of the virus from his lungs.)
I read that an exotic open-air animal market in Guangzhou, China is being investigated by WHO as possibly having something to do with the origin of the illness. (That story taught me a new word I didn't even know- zoonosis. It sounds like a good name for a band.)
Which isn't too hard to believe. Anyone who has watched any Nature episode on an endangered animal species has seen the part at the end that goes like this:
Unfortunately, the future of the [insert weird species here] is far from certain, because it is considered a delicacy in certain Asian countries.
(There's also a less common variant of the Nature show ending, where the species is an aphrodisiac and not a delicacy.)
Basically, the issue is that in Guangzhou, China there is a famous wet market where dozens of different animal species are for sale- rodents, birds, alligators, cats, badgers, dogs, porcupines, pigs, snakes, turtles, and other delicacies. They come from all over the world. They aren't frozen and packed or anything like that- they're running and fluttering around in their cages when you pick them out. Some of them have chewed their limbs off in attempts to escape traps. They are either butchered on the spot or you take them home still alive and kill them yourself. The emphasis is on freshness.
Of course this grossed out the tourists, not to mention the people who make Nature documentaries. So the Chinese authorities (in typical fashion) cracked down on the market two years ago by forcing it to move out of sight of foreigners. It was moved from an outdoor park setting into an enclosed building two years ago. WHO thinks the move to an indoor setting would have made the risk of zoonosis worse.
The first known SARS patient got sick in November. He lived 12 miles away, but had been in Guangzhou and received treatment there.